I was running the 5932 build of PCSx2 from the SVN. All of the games ran full speed at 60fps, with each sequel requiring different settings.

Jak & Daxter:

Only bothersome bug is the missing/black eyes, requiring DX9/11 software mode to fix. In DX9 SW mode, there was a weird blocky shadow over the characters, which is fixed by running it in DX11 SW mode. Personally, I played it in DX11 HW mode at 4x native resolution with no HW hacks enabled. EE cycle rate was set to 1, with VU Cycle Stealing on 0, and all speedhacks enabled. Setting VU0 to SuperVU made no difference, so I set it back to MicroVU. The game played perfectly with no hiccups.

Jak 2:

Still has the missing eyes bug from J&D, plus red lines across every patch of water. Also fixed by running in DX9/11 SW mode. For some reason, the blocky shadow doesn't disappear in DX11 SW mode like in J&D, so the only way to fix it is to run it in DX11 HW mode or DX9 HW mode with Texture Filtering, Allow 8-bit textures, Logarithmic Z, Alpha Correction and Enable HW hacks checked. All HW Hacks checked except 'Nvidia Hack' and 'Disable CRC's.' EE Cycle Rate set to 3, VU Cycle Stealing set to 1, and all speedhacks enabled.

Jak 3:

Missing eyes, but no striped water. Instead, the wasteland sand turns either black or dark brown. Fixed by running in SW mode. All other settings set to the same as Jak 2, but VU Cycle Stealing set to 0. For some reason, it started to lag up occasionally after going halfway through the game even while running at 60fps, but it was still playable.

I played all of them with a monoprice PS3 controller. Before you think this game will run great on your PC, you'll have to check my PC specs. Compared to other games I've played, Jak required a lot of tweaking to run perfectly. You might require slightly different settings, but my settings are what you should start from.